Oracle HealthFacts: Laboratory molecular biomarker results analysis: Troponin biomarkers

Read data file.

## [1] "Columns: patient_id, encounter_id, admitted_dt_tm, age_in_years, age_in_days, patient_type_id, loinc_code, accession, lab_procedure_id, lab_procedure_mnemonic, unit_display, numeric_result"

## [1] "Patients: 214660; Encounters: 241460"

Tests in this dataset.

Lab	N
Troponin I	167280
Troponin T S/Pl	166588
Troponin	52788
Troponin I SerPl aCnc	15398
Troponin I Bld Quant	4455
Troponin I Ser/plasma DL<=0.01 ng/mL Quant	122
Title:
Lab tests in dataset, with value counts

Define biomarker[s] of interest.

## Biomarker of interest: "Troponin I"

## Biomarker of interest: "Troponin T S/Pl"

Select dataset for biomarker[s] of interest.

i	labs	valcount	units	pref_units	pref_units_valcount	mean	median	sd
1	Troponin I	167280	ng/mL	ng/mL	167280	1.0339	0.02	11.0724
2	Troponin T S/Pl	166588	ng/mL, ng/dL	ng/mL	166326	0.0805	0.01	0.6062
Title:
Summary of data for biomarker[s] of interest (2)

## Troponin I; N = 167280; min = 0.0000; max = 1182.9400; mean = 1.0339; median = 0.0200; sd = 11.0724

## Troponin T S/Pl; N = 166588; min = 0.0000; max = 68.3000; mean = 0.0805; median = 0.0100; sd = 0.6058

Remove extreme and likely spurious values

## [1] "Troponin T S/Pl; N = 43823; min = 0.0110; max = 0.0790; mean = 0.0283; median = 0.0200; sd = 0.0146"

Troponin T S/Pl: distribution percentiles

percentiles	values
0%	0.011
10%	0.020
20%	0.020
30%	0.020
40%	0.020
50%	0.020
60%	0.020
70%	0.030
80%	0.040
90%	0.050
100%	0.079

## [1] "Columns: patient_id, patient_type_id, patient_type_desc, gender, race, ethnicity, age_mid_year, exclusion_flag, agegroup"

Patient cohort descriptive statistics

## [1] "Patients: 41331; Not-excluded: 24947 (60.4%)"

Troponin T S/Pl cohort, pre-exclusion, Gender distribution

Gender	n_pt
Female	22682
Male	18639
Unknown/Invalid	10

Exclude patients based on exclusion criteria (diagnosis related to heart disease)

Troponin T S/Pl cohort, Gender distribution

Gender	n_pt
Female	14665
Male	10272
Unknown/Invalid	10

Troponin T S/Pl cohort, Patient_type distribution

Patient_type	n_pt
Emergency	15732
Inpatient	5454
Observation	2019
Outpatient	719
Observation / Short stay / 24 hr stay	409
Non-Patient	153
Clinic	125
Laboratory	88
Not Mapped	69
Other Specialty	52
Unknown / Invalid	32
Community	25
Outpatient Surgery	20
HLA QC	18
Radiology	13
Day Surgery	6
Recurring	5
Urgent	4
Skilled Nursing Facility	3
Billing	1

Troponin T S/Pl cohort, Race distribution

Race	n_pt
Caucasian	18379
African American	4704
Other	739
Unknown	370
Asian	251
Native American	246
Hispanic	117
Asian/Pacific Islander	40
NULL	34
Biracial	32
Pacific Islander	21
Not Mapped	14

Age distribution

## [1] "Age_mid_year: N = 24330; min = 1.0; max = 90.6; mean = 62.2; median = 63.1; sd = 18.1"

Troponin T S/Pl cohort, Age_mid_year: distribution percentiles

percentiles	values
0%	0.96
10%	36.61
20%	46.21
30%	53.01
40%	58.18
50%	63.10
60%	68.69
70%	73.99
80%	79.52
90%	85.98
100%	90.56

Remove patients with unknown gender or age

## [1] "Excluding patients with unknown gender: 10 / 24947 (0.0%) excluded"

## [1] "Excluding patients with unknown agegroup: 617 / 24947 (2.5%) excluded"

Stratified statistics and distributions

Initially, for sex and age-group. First merge lab value table with stratification variables.

## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL
## WARNING: multiple units: ng/dL; ng/mL

Troponin T S/Pl: Normal-physiological healthy patient cohort, stratified statistics

i	sex	agegroup	valcount	units	mean	median	sd
1	Female	00-09	0	ng/dL; ng/mL	NaN	NA	NA
2	Male	00-09	1	ng/dL; ng/mL	0.0100	0.010	NA
3	Female	10-19	22	ng/dL; ng/mL	0.0364	0.010	0.1214
4	Male	10-19	14	ng/dL; ng/mL	0.0100	0.010	0.0000
5	Female	20-29	230	ng/dL; ng/mL	0.0192	0.010	0.0415
6	Male	20-29	142	ng/dL; ng/mL	0.0341	0.010	0.0888
7	Female	30-39	432	ng/dL; ng/mL	0.0168	0.010	0.0444
8	Male	30-39	352	ng/dL; ng/mL	0.0244	0.010	0.0664
9	Female	40-49	789	ng/dL; ng/mL	0.0250	0.010	0.0836
10	Male	40-49	476	ng/dL; ng/mL	0.0390	0.010	0.0754
11	Female	50-59	1097	ng/dL; ng/mL	0.0162	0.010	0.0483
12	Male	50-59	1019	ng/dL; ng/mL	0.0285	0.010	0.0852
13	Female	60-69	1123	ng/dL; ng/mL	0.0285	0.010	0.0743
14	Male	60-69	810	ng/dL; ng/mL	0.0197	0.010	0.0321
15	Female	70-79	1047	ng/dL; ng/mL	0.0215	0.010	0.0538
16	Male	70-79	744	ng/dL; ng/mL	0.0315	0.010	0.0842
17	Female	80-89	935	ng/dL; ng/mL	0.0278	0.010	0.1506
18	Male	80-89	531	ng/dL; ng/mL	0.0380	0.010	0.0946
19	Female	90+	360	ng/dL; ng/mL	0.0455	0.010	0.2404
20	Male	90+	171	ng/dL; ng/mL	0.0453	0.015	0.1529